Abstract

We present a revised version of a Monte Carlo simulation model for RNA molecules that was introduced in a previous communication [O. Taxilaga-Zetina, P. Pliego-Pastrana, and M. D. Carbajal-Tinoco, Phys. Rev. E81, 041914 (2010)]. The basic model consists of a series of knowledge-based pair potentials that were obtained from the statistical analysis of large RNAs belonging to the Protein Data Bank. These effective interactions are then used to dress a polymeric chain that reproduces relatively simple secondary structures (e.g., small hairpins). In order to describe more complicated three-dimensional structures such as pseudo-knots, here we include orientational information for the interaction between nucleotides forming hydrogen bonds, as in the case of the Watson-Crick base pairs. As a result, the simulated molecules obtained through the modified model are now consistent with their corresponding experimental configurations.

The authors want to thank Mario Villada-Balbuena for helpful discussions. P.P.-P. acknowledges PROMEP (Mexico) for supporting this work under grant UAEH-PTC-543. O.T.-Z. and M.D.C.-T. acknowledge CONACyT (Mexico) for the support through both a fellowship and Grant No. 152532, respectively. Some calculations were performed at the cluster Xiuhcoatl of Cinvestav and the rest of them at the UAEH.